{"repo":"nf-core/readsimulator","free":true,"listed":false,"github":"https://github.com/nf-core/readsimulator","clone":"git clone https://github.com/nf-core/readsimulator.git","description":"A pipeline to simulate sequencing reads, such as Amplicon, Target Capture, Metagenome, and Whole genome data.","language":"Nextflow","stars":35,"topics":["nextflow","nf-core","pipeline","workflow"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/readsimulator is a pipeline to simulate sequencing reads. The pipeline currently supports simulating amplicon, target capture, metagenome, and wholegenome data. It takes a samplesheet with sample names and seeds for random generation to produce simulated FASTQ files and a samplesheet that contains the paths to the FASTQ files. Amplicon simulation steps 1. Create reference database for amplicon-based sequencing ( CRABS ) 2. Simulate amplicon Illumina reads ( art illumina ) 3. Create samplesheet with sample names and paths to simulated read files (header = sample,fastq 1,fastq 2) 4. Simulated read QC ( FastQC ) 5. Present QC for simulated reads ( MultiQC ) Target capture simulation steps 1. Align probes to genome ( Bowtie2 ) 2. Get SAM index ( SAMtools ) 3. Simulate target capture reads (Illumina (default) or Pacbio) ( Japsa capsim ) 4. Create samplesheet with sample names and paths to simulated read files (header = sample,fastq 1,fastq 2) 5. Simulated read QC ( FastQC ) 6. Present QC for simulated reads ( MultiQC ) Metagenome simulation steps 1. Simulate metagenome Illumina reads ( InsilicoSeq Generate ) 2. Create samplesheet with sample names and paths to simulated read files (header = sample,fastq 1,fastq 2) 3. Simulated read QC ( FastQC ) 4. Present QC for simulated reads ( MultiQC ) Wholegenome simulation steps 1. Simulate wholegenome reads ( wgsim ) 2. Create samplesheet with sample names and paths to simulated read files (header = sample,fastq 1,fast","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/readsimulator/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}